Multiple sequence alignment - TraesCS7D01G109100

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7D01G109100 chr7D 100.000 3140 0 0 1 3140 65733308 65730169 0.000000e+00 5799.0
1 TraesCS7D01G109100 chr7B 91.499 2588 135 39 576 3140 7358584 7356059 0.000000e+00 3482.0
2 TraesCS7D01G109100 chr7B 85.542 581 40 18 1 549 7363408 7362840 4.540000e-158 568.0
3 TraesCS7D01G109100 chr7A 90.416 1586 100 29 576 2141 69974276 69975829 0.000000e+00 2039.0
4 TraesCS7D01G109100 chr7A 83.799 358 31 13 2159 2501 69829461 69829806 6.540000e-82 315.0
5 TraesCS7D01G109100 chr7A 87.931 116 9 3 2377 2487 70043418 70043533 7.070000e-27 132.0
6 TraesCS7D01G109100 chr7A 75.000 164 28 13 1734 1889 70095701 70095859 2.610000e-06 63.9
7 TraesCS7D01G109100 chr1D 77.226 584 93 29 2543 3097 204803262 204803834 3.930000e-79 305.0
8 TraesCS7D01G109100 chr1D 75.081 618 115 19 2550 3136 124093643 124094252 5.200000e-63 252.0
9 TraesCS7D01G109100 chr6D 76.424 632 108 20 2540 3136 361545019 361545644 1.420000e-78 303.0
10 TraesCS7D01G109100 chr6D 87.356 87 11 0 2808 2894 417686819 417686733 1.990000e-17 100.0
11 TraesCS7D01G109100 chr2D 77.298 533 73 30 2623 3116 169024045 169023522 1.440000e-68 270.0
12 TraesCS7D01G109100 chr6B 74.840 624 110 32 2543 3140 144036713 144037315 4.050000e-59 239.0
13 TraesCS7D01G109100 chr4D 74.326 631 118 30 2539 3136 150979283 150978664 8.760000e-56 228.0
14 TraesCS7D01G109100 chrUn 73.469 588 121 22 2576 3134 76980293 76979712 4.130000e-44 189.0
15 TraesCS7D01G109100 chr3B 73.638 569 109 29 2585 3129 638958669 638958118 6.920000e-42 182.0
16 TraesCS7D01G109100 chr3A 76.068 351 61 10 2543 2875 389122622 389122277 9.010000e-36 161.0
17 TraesCS7D01G109100 chr3A 72.484 636 108 43 2543 3136 673468432 673469042 3.260000e-30 143.0
18 TraesCS7D01G109100 chr4A 86.842 114 15 0 2781 2894 4015456 4015343 9.140000e-26 128.0
19 TraesCS7D01G109100 chr1A 74.160 387 59 21 2619 2976 579996157 579996531 4.250000e-24 122.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G109100 chr7D 65730169 65733308 3139 True 5799 5799 100.000 1 3140 1 chr7D.!!$R1 3139
1 TraesCS7D01G109100 chr7B 7356059 7358584 2525 True 3482 3482 91.499 576 3140 1 chr7B.!!$R1 2564
2 TraesCS7D01G109100 chr7B 7362840 7363408 568 True 568 568 85.542 1 549 1 chr7B.!!$R2 548
3 TraesCS7D01G109100 chr7A 69974276 69975829 1553 False 2039 2039 90.416 576 2141 1 chr7A.!!$F2 1565
4 TraesCS7D01G109100 chr1D 204803262 204803834 572 False 305 305 77.226 2543 3097 1 chr1D.!!$F2 554
5 TraesCS7D01G109100 chr1D 124093643 124094252 609 False 252 252 75.081 2550 3136 1 chr1D.!!$F1 586
6 TraesCS7D01G109100 chr6D 361545019 361545644 625 False 303 303 76.424 2540 3136 1 chr6D.!!$F1 596
7 TraesCS7D01G109100 chr2D 169023522 169024045 523 True 270 270 77.298 2623 3116 1 chr2D.!!$R1 493
8 TraesCS7D01G109100 chr6B 144036713 144037315 602 False 239 239 74.840 2543 3140 1 chr6B.!!$F1 597
9 TraesCS7D01G109100 chr4D 150978664 150979283 619 True 228 228 74.326 2539 3136 1 chr4D.!!$R1 597

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
559 591 0.032952 AACTTCGCGCACAGGTAAGA 59.967 50.0 8.75 0.0 0.0 2.10 F
560 592 0.032952 ACTTCGCGCACAGGTAAGAA 59.967 50.0 8.75 0.0 0.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1389 1454 0.462759 GGCCGATGGACTTGAGGAAG 60.463 60.000 0.0 0.0 35.07 3.46 R
2501 2569 1.066573 AGGTCGCTGTTGGAGATTCTG 60.067 52.381 0.0 0.0 0.00 3.02 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
100 101 8.061125 AGCAAAATTCAAAACTATTTCGTGTC 57.939 30.769 0.00 0.00 0.00 3.67
108 109 7.753659 TCAAAACTATTTCGTGTCTGTCAAAA 58.246 30.769 0.00 0.00 0.00 2.44
109 110 8.237949 TCAAAACTATTTCGTGTCTGTCAAAAA 58.762 29.630 0.00 0.00 0.00 1.94
120 121 6.692681 CGTGTCTGTCAAAAATTGTTCTGAAT 59.307 34.615 0.00 0.00 0.00 2.57
124 125 9.950680 GTCTGTCAAAAATTGTTCTGAATTAGA 57.049 29.630 0.00 0.00 0.00 2.10
205 209 7.833786 TGTCGATACAGTTAGTTCCAAAGTAT 58.166 34.615 0.00 0.00 0.00 2.12
208 212 7.699391 TCGATACAGTTAGTTCCAAAGTATTCG 59.301 37.037 0.00 0.00 0.00 3.34
212 216 2.094762 AGTTCCAAAGTATTCGCGCT 57.905 45.000 5.56 0.00 0.00 5.92
222 226 1.951181 TATTCGCGCTGCACGTTCAC 61.951 55.000 10.05 0.00 46.11 3.18
239 243 4.493545 CGTTCACCATGAGCGGTAATTAAC 60.494 45.833 7.12 0.00 45.30 2.01
242 246 3.560068 CACCATGAGCGGTAATTAACTCC 59.440 47.826 0.00 0.00 37.07 3.85
255 259 6.156775 GGTAATTAACTCCAGTGGGTAGGTAA 59.843 42.308 9.92 10.00 32.08 2.85
291 295 2.202892 GGATGGCGAGTTCGGACC 60.203 66.667 3.50 0.00 40.23 4.46
301 305 1.725164 GAGTTCGGACCTTTGCTAACG 59.275 52.381 0.00 0.00 0.00 3.18
349 355 7.958112 AAAAATGTTCACGTGTGTTTACTAC 57.042 32.000 16.51 3.24 0.00 2.73
365 371 8.169268 GTGTTTACTACTTGCATGTAGATGTTC 58.831 37.037 34.20 22.44 41.63 3.18
375 381 9.630098 CTTGCATGTAGATGTTCAAAAATTACT 57.370 29.630 1.37 0.00 31.50 2.24
378 384 9.210426 GCATGTAGATGTTCAAAAATTACTACG 57.790 33.333 1.37 0.00 33.91 3.51
438 470 5.765576 TTGTGGCTAGGTACCTATTTCAA 57.234 39.130 22.02 19.02 0.00 2.69
447 479 7.010830 GCTAGGTACCTATTTCAAAAACTACGG 59.989 40.741 22.02 5.79 0.00 4.02
455 487 2.025155 TCAAAAACTACGGCCAGCAAA 58.975 42.857 2.24 0.00 0.00 3.68
456 488 2.427453 TCAAAAACTACGGCCAGCAAAA 59.573 40.909 2.24 0.00 0.00 2.44
477 509 2.222227 AAAAGCCTCCAATGGACCTC 57.778 50.000 0.00 0.00 0.00 3.85
478 510 0.035056 AAAGCCTCCAATGGACCTCG 60.035 55.000 0.00 0.00 0.00 4.63
520 552 4.974721 CAGCCGGCCCCTGTTTGT 62.975 66.667 26.15 0.00 0.00 2.83
553 585 4.099924 CGAAAACTTCGCGCACAG 57.900 55.556 8.75 4.48 46.97 3.66
554 586 1.438710 CGAAAACTTCGCGCACAGG 60.439 57.895 8.75 0.00 46.97 4.00
555 587 1.647084 GAAAACTTCGCGCACAGGT 59.353 52.632 8.75 0.00 0.00 4.00
556 588 0.863144 GAAAACTTCGCGCACAGGTA 59.137 50.000 8.75 0.00 0.00 3.08
557 589 1.262151 GAAAACTTCGCGCACAGGTAA 59.738 47.619 8.75 0.00 0.00 2.85
558 590 0.865769 AAACTTCGCGCACAGGTAAG 59.134 50.000 8.75 0.00 0.00 2.34
559 591 0.032952 AACTTCGCGCACAGGTAAGA 59.967 50.000 8.75 0.00 0.00 2.10
560 592 0.032952 ACTTCGCGCACAGGTAAGAA 59.967 50.000 8.75 0.00 0.00 2.52
561 593 1.144969 CTTCGCGCACAGGTAAGAAA 58.855 50.000 8.75 0.00 0.00 2.52
562 594 1.529438 CTTCGCGCACAGGTAAGAAAA 59.471 47.619 8.75 0.00 0.00 2.29
563 595 1.584175 TCGCGCACAGGTAAGAAAAA 58.416 45.000 8.75 0.00 0.00 1.94
564 596 1.262151 TCGCGCACAGGTAAGAAAAAC 59.738 47.619 8.75 0.00 0.00 2.43
565 597 1.003331 CGCGCACAGGTAAGAAAAACA 60.003 47.619 8.75 0.00 0.00 2.83
566 598 2.650608 GCGCACAGGTAAGAAAAACAG 58.349 47.619 0.30 0.00 0.00 3.16
567 599 2.289547 GCGCACAGGTAAGAAAAACAGA 59.710 45.455 0.30 0.00 0.00 3.41
568 600 3.242936 GCGCACAGGTAAGAAAAACAGAA 60.243 43.478 0.30 0.00 0.00 3.02
569 601 4.732355 GCGCACAGGTAAGAAAAACAGAAA 60.732 41.667 0.30 0.00 0.00 2.52
570 602 5.336744 CGCACAGGTAAGAAAAACAGAAAA 58.663 37.500 0.00 0.00 0.00 2.29
571 603 5.229260 CGCACAGGTAAGAAAAACAGAAAAC 59.771 40.000 0.00 0.00 0.00 2.43
572 604 6.330278 GCACAGGTAAGAAAAACAGAAAACT 58.670 36.000 0.00 0.00 0.00 2.66
573 605 6.811665 GCACAGGTAAGAAAAACAGAAAACTT 59.188 34.615 0.00 0.00 0.00 2.66
574 606 7.009265 GCACAGGTAAGAAAAACAGAAAACTTC 59.991 37.037 0.00 0.00 0.00 3.01
653 692 4.612536 CGCCATTGAATCGCGCCC 62.613 66.667 3.97 0.00 39.39 6.13
688 727 3.855950 CGAACTTACGGTTGATCAGTACC 59.144 47.826 6.51 6.51 38.41 3.34
695 734 1.822990 GGTTGATCAGTACCTGACCGA 59.177 52.381 9.02 0.00 43.63 4.69
696 735 2.416972 GGTTGATCAGTACCTGACCGAC 60.417 54.545 9.02 0.00 43.63 4.79
697 736 1.471119 TGATCAGTACCTGACCGACC 58.529 55.000 0.00 0.00 43.63 4.79
698 737 0.381089 GATCAGTACCTGACCGACCG 59.619 60.000 0.00 0.00 43.63 4.79
699 738 1.035932 ATCAGTACCTGACCGACCGG 61.036 60.000 6.94 6.94 43.63 5.28
700 739 1.676635 CAGTACCTGACCGACCGGA 60.677 63.158 16.07 0.00 38.96 5.14
702 741 1.377725 GTACCTGACCGACCGGAGA 60.378 63.158 16.07 0.00 38.96 3.71
703 742 1.377725 TACCTGACCGACCGGAGAC 60.378 63.158 16.07 6.76 38.96 3.36
726 765 2.352960 GTGCTAGCTAGGTTGCATGAAC 59.647 50.000 28.65 15.33 37.76 3.18
801 842 3.289836 TCGGAGGTGGTTGTTCGATATA 58.710 45.455 0.00 0.00 0.00 0.86
802 843 3.893200 TCGGAGGTGGTTGTTCGATATAT 59.107 43.478 0.00 0.00 0.00 0.86
803 844 5.072055 TCGGAGGTGGTTGTTCGATATATA 58.928 41.667 0.00 0.00 0.00 0.86
820 861 0.534427 ATAGATCGTCGGCGGTGAGA 60.534 55.000 10.62 1.77 38.89 3.27
821 862 1.158484 TAGATCGTCGGCGGTGAGAG 61.158 60.000 10.62 0.00 38.89 3.20
822 863 4.194720 ATCGTCGGCGGTGAGAGC 62.195 66.667 10.62 0.00 38.89 4.09
824 865 3.506096 CGTCGGCGGTGAGAGCTA 61.506 66.667 7.21 0.00 34.52 3.32
825 866 2.882876 GTCGGCGGTGAGAGCTAA 59.117 61.111 7.21 0.00 34.52 3.09
826 867 1.437986 GTCGGCGGTGAGAGCTAAT 59.562 57.895 7.21 0.00 34.52 1.73
910 951 5.279306 GGGCTCTCATCCACGTTATATACAA 60.279 44.000 0.00 0.00 0.00 2.41
931 972 0.249114 TTCGTGCACAGCGTAGTTGA 60.249 50.000 18.64 0.00 42.98 3.18
964 1021 0.526310 CTAGAGCGCGTGCAAGATCA 60.526 55.000 24.79 0.67 46.23 2.92
965 1022 0.526310 TAGAGCGCGTGCAAGATCAG 60.526 55.000 24.79 0.00 46.23 2.90
966 1023 2.806856 GAGCGCGTGCAAGATCAGG 61.807 63.158 24.79 0.00 46.23 3.86
967 1024 3.121030 GCGCGTGCAAGATCAGGT 61.121 61.111 17.66 0.00 42.15 4.00
968 1025 2.780643 CGCGTGCAAGATCAGGTG 59.219 61.111 2.99 0.00 0.00 4.00
969 1026 2.482374 GCGTGCAAGATCAGGTGC 59.518 61.111 2.99 8.62 41.29 5.01
970 1027 2.037136 GCGTGCAAGATCAGGTGCT 61.037 57.895 2.99 0.00 41.48 4.40
971 1028 0.740868 GCGTGCAAGATCAGGTGCTA 60.741 55.000 2.99 2.39 41.48 3.49
972 1029 1.284657 CGTGCAAGATCAGGTGCTAG 58.715 55.000 14.68 7.07 41.48 3.42
973 1030 1.134995 CGTGCAAGATCAGGTGCTAGA 60.135 52.381 14.68 0.00 41.48 2.43
974 1031 2.482664 CGTGCAAGATCAGGTGCTAGAT 60.483 50.000 14.68 0.00 41.48 1.98
975 1032 3.129871 GTGCAAGATCAGGTGCTAGATC 58.870 50.000 14.68 0.00 41.48 2.75
976 1033 2.767960 TGCAAGATCAGGTGCTAGATCA 59.232 45.455 14.68 0.00 42.36 2.92
977 1034 3.198417 TGCAAGATCAGGTGCTAGATCAA 59.802 43.478 14.68 0.00 42.36 2.57
978 1035 3.559242 GCAAGATCAGGTGCTAGATCAAC 59.441 47.826 8.37 0.00 42.36 3.18
979 1036 4.125703 CAAGATCAGGTGCTAGATCAACC 58.874 47.826 0.00 0.00 42.36 3.77
980 1037 2.363680 AGATCAGGTGCTAGATCAACCG 59.636 50.000 0.00 0.00 42.36 4.44
981 1038 1.847328 TCAGGTGCTAGATCAACCGA 58.153 50.000 0.00 0.00 0.00 4.69
1242 1307 2.527123 TACTTCGGCCACCCCACA 60.527 61.111 2.24 0.00 0.00 4.17
1290 1355 2.507324 GACTTCCTCGCGCAGTCC 60.507 66.667 8.75 0.00 32.26 3.85
1305 1370 2.687566 TCCCTCGGCCTCCCTTTC 60.688 66.667 0.00 0.00 0.00 2.62
1389 1454 4.719369 ACGGCGCTGGACTTCGAC 62.719 66.667 22.44 0.00 0.00 4.20
1452 1517 2.956987 GCCATCAACGTGCAGCTT 59.043 55.556 0.00 0.00 0.00 3.74
1596 1661 3.423154 GGCTTCAACGTCAGCCGG 61.423 66.667 15.42 0.00 46.19 6.13
1728 1793 0.464916 TCGCGCTCTACCTCACCATA 60.465 55.000 5.56 0.00 0.00 2.74
1827 1892 2.268280 CTGCTCCAGGACAGGCTG 59.732 66.667 14.16 14.16 0.00 4.85
2016 2081 4.115199 GGGATGAAGGGCGCCACT 62.115 66.667 30.85 20.16 0.00 4.00
2173 2238 1.003580 ACGGCAGGAGAATGAACATGT 59.996 47.619 0.00 0.00 0.00 3.21
2266 2333 5.434408 CTTTAGCCCTTTACCTTTCGGTAT 58.566 41.667 0.00 0.00 44.96 2.73
2269 2336 2.686405 GCCCTTTACCTTTCGGTATTGG 59.314 50.000 0.00 0.00 44.96 3.16
2330 2397 0.250553 CCAGCCCAGTGTCCGTTTTA 60.251 55.000 0.00 0.00 0.00 1.52
2476 2544 7.614124 TTTATGACCCGTTTGTAAAGTATCC 57.386 36.000 0.00 0.00 0.00 2.59
2481 2549 3.242608 CCCGTTTGTAAAGTATCCATGCG 60.243 47.826 0.00 0.00 0.00 4.73
2514 2582 4.910195 ACAACTATGCAGAATCTCCAACA 58.090 39.130 0.00 0.00 0.00 3.33
2601 2669 4.728882 GCTCCTCGCATACATTTCAACAAG 60.729 45.833 0.00 0.00 38.92 3.16
2757 2847 2.345244 CCACGAACTGCTCTGCCT 59.655 61.111 0.00 0.00 0.00 4.75
2767 2857 2.264794 CTCTGCCTTACCGCCGTT 59.735 61.111 0.00 0.00 0.00 4.44
2774 2864 2.437002 TTACCGCCGTTGCCATCC 60.437 61.111 0.00 0.00 0.00 3.51
2895 3001 3.524606 GCGCTGTACGGAGGGCTA 61.525 66.667 5.68 0.00 45.86 3.93
2896 3002 2.412112 CGCTGTACGGAGGGCTAC 59.588 66.667 5.68 0.00 38.44 3.58
2897 3003 2.813200 GCTGTACGGAGGGCTACC 59.187 66.667 5.68 0.00 0.00 3.18
2979 3085 4.509737 GGTGGAGTAGTCGCGGCC 62.510 72.222 7.31 0.00 0.00 6.13
3049 3173 0.460284 GACGTCTCCGCAATGGTGAT 60.460 55.000 8.70 0.00 41.99 3.06
3129 3253 2.280524 CGTCCGACTTGGCCAACA 60.281 61.111 16.05 0.00 37.80 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
70 71 8.538856 CGAAATAGTTTTGAATTTTGCTTGACA 58.461 29.630 0.00 0.00 0.00 3.58
163 167 4.264253 TCGACAGGTCCGAGTATTTTCTA 58.736 43.478 0.00 0.00 0.00 2.10
164 168 3.087031 TCGACAGGTCCGAGTATTTTCT 58.913 45.455 0.00 0.00 0.00 2.52
165 169 3.498927 TCGACAGGTCCGAGTATTTTC 57.501 47.619 0.00 0.00 0.00 2.29
166 170 4.400251 TGTATCGACAGGTCCGAGTATTTT 59.600 41.667 0.00 0.00 39.55 1.82
191 195 3.369756 CAGCGCGAATACTTTGGAACTAA 59.630 43.478 12.10 0.00 0.00 2.24
205 209 3.995669 GTGAACGTGCAGCGCGAA 61.996 61.111 33.96 16.13 46.11 4.70
208 212 3.726517 ATGGTGAACGTGCAGCGC 61.727 61.111 20.34 0.00 46.11 5.92
212 216 2.316867 CGCTCATGGTGAACGTGCA 61.317 57.895 0.00 0.00 36.01 4.57
217 221 4.634443 AGTTAATTACCGCTCATGGTGAAC 59.366 41.667 0.00 0.00 43.68 3.18
222 226 3.804036 TGGAGTTAATTACCGCTCATGG 58.196 45.455 10.94 0.00 0.00 3.66
239 243 3.103080 AGAGTTACCTACCCACTGGAG 57.897 52.381 0.00 0.00 34.81 3.86
242 246 7.621796 AGATAAAAAGAGTTACCTACCCACTG 58.378 38.462 0.00 0.00 0.00 3.66
255 259 5.221541 CCATCCGCCTCTAGATAAAAAGAGT 60.222 44.000 0.00 0.00 38.03 3.24
259 263 3.740115 GCCATCCGCCTCTAGATAAAAA 58.260 45.455 0.00 0.00 0.00 1.94
264 268 1.228583 TCGCCATCCGCCTCTAGAT 60.229 57.895 0.00 0.00 36.73 1.98
267 271 1.735376 GAACTCGCCATCCGCCTCTA 61.735 60.000 0.00 0.00 36.73 2.43
272 276 4.508128 TCCGAACTCGCCATCCGC 62.508 66.667 0.00 0.00 38.18 5.54
274 278 2.202892 GGTCCGAACTCGCCATCC 60.203 66.667 0.00 0.00 38.18 3.51
287 291 2.033194 AGCGCGTTAGCAAAGGTCC 61.033 57.895 8.43 0.00 45.49 4.46
288 292 1.132640 CAGCGCGTTAGCAAAGGTC 59.867 57.895 8.43 0.00 45.49 3.85
291 295 0.454957 AATGCAGCGCGTTAGCAAAG 60.455 50.000 21.85 0.00 45.49 2.77
327 331 6.913873 AGTAGTAAACACACGTGAACATTT 57.086 33.333 25.01 17.22 0.00 2.32
329 333 5.277154 GCAAGTAGTAAACACACGTGAACAT 60.277 40.000 25.01 8.19 0.00 2.71
330 334 4.033129 GCAAGTAGTAAACACACGTGAACA 59.967 41.667 25.01 0.00 0.00 3.18
331 335 4.033129 TGCAAGTAGTAAACACACGTGAAC 59.967 41.667 25.01 11.51 0.00 3.18
333 337 3.783191 TGCAAGTAGTAAACACACGTGA 58.217 40.909 25.01 0.00 0.00 4.35
334 338 4.025229 ACATGCAAGTAGTAAACACACGTG 60.025 41.667 15.48 15.48 0.00 4.49
335 339 4.124238 ACATGCAAGTAGTAAACACACGT 58.876 39.130 0.00 0.00 0.00 4.49
337 341 7.117812 ACATCTACATGCAAGTAGTAAACACAC 59.882 37.037 24.14 0.00 41.68 3.82
349 355 9.630098 AGTAATTTTTGAACATCTACATGCAAG 57.370 29.630 0.00 0.00 32.57 4.01
413 419 6.544650 TGAAATAGGTACCTAGCCACAAAAA 58.455 36.000 25.40 1.88 31.45 1.94
426 458 5.412286 TGGCCGTAGTTTTTGAAATAGGTAC 59.588 40.000 0.00 0.00 0.00 3.34
473 505 0.244994 GATGTGCACTGAGACGAGGT 59.755 55.000 19.41 0.00 0.00 3.85
477 509 2.636768 TGTAGATGTGCACTGAGACG 57.363 50.000 19.41 0.00 0.00 4.18
478 510 2.606725 GCATGTAGATGTGCACTGAGAC 59.393 50.000 19.41 11.43 40.94 3.36
546 578 2.289547 TCTGTTTTTCTTACCTGTGCGC 59.710 45.455 0.00 0.00 0.00 6.09
549 581 7.218204 CGAAGTTTTCTGTTTTTCTTACCTGTG 59.782 37.037 0.00 0.00 0.00 3.66
550 582 7.248437 CGAAGTTTTCTGTTTTTCTTACCTGT 58.752 34.615 0.00 0.00 0.00 4.00
551 583 6.196538 GCGAAGTTTTCTGTTTTTCTTACCTG 59.803 38.462 0.00 0.00 0.00 4.00
552 584 6.263344 GCGAAGTTTTCTGTTTTTCTTACCT 58.737 36.000 0.00 0.00 0.00 3.08
553 585 5.457799 GGCGAAGTTTTCTGTTTTTCTTACC 59.542 40.000 0.00 0.00 0.00 2.85
554 586 5.457799 GGGCGAAGTTTTCTGTTTTTCTTAC 59.542 40.000 0.00 0.00 0.00 2.34
555 587 5.125739 TGGGCGAAGTTTTCTGTTTTTCTTA 59.874 36.000 0.00 0.00 0.00 2.10
556 588 4.081917 TGGGCGAAGTTTTCTGTTTTTCTT 60.082 37.500 0.00 0.00 0.00 2.52
557 589 3.445805 TGGGCGAAGTTTTCTGTTTTTCT 59.554 39.130 0.00 0.00 0.00 2.52
558 590 3.550275 GTGGGCGAAGTTTTCTGTTTTTC 59.450 43.478 0.00 0.00 0.00 2.29
559 591 3.517602 GTGGGCGAAGTTTTCTGTTTTT 58.482 40.909 0.00 0.00 0.00 1.94
560 592 2.478879 CGTGGGCGAAGTTTTCTGTTTT 60.479 45.455 0.00 0.00 41.33 2.43
561 593 1.064952 CGTGGGCGAAGTTTTCTGTTT 59.935 47.619 0.00 0.00 41.33 2.83
562 594 0.661020 CGTGGGCGAAGTTTTCTGTT 59.339 50.000 0.00 0.00 41.33 3.16
563 595 0.179067 TCGTGGGCGAAGTTTTCTGT 60.179 50.000 0.00 0.00 44.92 3.41
564 596 2.612200 TCGTGGGCGAAGTTTTCTG 58.388 52.632 0.00 0.00 44.92 3.02
632 671 3.101209 GCGATTCAATGGCGAGCA 58.899 55.556 0.00 0.00 0.00 4.26
653 692 1.965083 AAGTTCGTCGTCGTCTCATG 58.035 50.000 1.33 0.00 38.33 3.07
697 736 1.649815 CTAGCTAGCACCGTCTCCG 59.350 63.158 18.83 0.00 0.00 4.63
698 737 0.752376 ACCTAGCTAGCACCGTCTCC 60.752 60.000 18.83 0.00 0.00 3.71
699 738 1.104630 AACCTAGCTAGCACCGTCTC 58.895 55.000 18.83 0.00 0.00 3.36
700 739 0.818296 CAACCTAGCTAGCACCGTCT 59.182 55.000 18.83 0.00 0.00 4.18
702 741 1.218316 GCAACCTAGCTAGCACCGT 59.782 57.895 18.83 6.12 0.00 4.83
703 742 0.179073 ATGCAACCTAGCTAGCACCG 60.179 55.000 18.83 5.42 40.14 4.94
704 743 1.134401 TCATGCAACCTAGCTAGCACC 60.134 52.381 18.83 3.90 40.14 5.01
705 744 2.315925 TCATGCAACCTAGCTAGCAC 57.684 50.000 18.83 4.60 40.14 4.40
706 745 2.632377 GTTCATGCAACCTAGCTAGCA 58.368 47.619 18.83 11.43 41.73 3.49
707 746 1.594862 CGTTCATGCAACCTAGCTAGC 59.405 52.381 15.74 6.62 34.99 3.42
708 747 1.594862 GCGTTCATGCAACCTAGCTAG 59.405 52.381 14.20 14.20 34.99 3.42
709 748 1.066502 TGCGTTCATGCAACCTAGCTA 60.067 47.619 0.00 0.00 43.02 3.32
710 749 0.321564 TGCGTTCATGCAACCTAGCT 60.322 50.000 0.00 0.00 43.02 3.32
801 842 0.534427 TCTCACCGCCGACGATCTAT 60.534 55.000 0.00 0.00 43.93 1.98
802 843 1.153309 TCTCACCGCCGACGATCTA 60.153 57.895 0.00 0.00 43.93 1.98
803 844 2.437895 TCTCACCGCCGACGATCT 60.438 61.111 0.00 0.00 43.93 2.75
821 862 2.541120 CGCTCCAGCTGGCATTAGC 61.541 63.158 28.91 27.58 44.01 3.09
822 863 0.879400 CTCGCTCCAGCTGGCATTAG 60.879 60.000 28.91 20.45 39.32 1.73
823 864 1.144716 CTCGCTCCAGCTGGCATTA 59.855 57.895 28.91 9.99 39.32 1.90
824 865 2.124819 CTCGCTCCAGCTGGCATT 60.125 61.111 28.91 0.00 39.32 3.56
825 866 3.079478 TCTCGCTCCAGCTGGCAT 61.079 61.111 28.91 0.00 39.32 4.40
826 867 3.767806 CTCTCGCTCCAGCTGGCA 61.768 66.667 28.91 15.63 39.32 4.92
952 993 0.740868 TAGCACCTGATCTTGCACGC 60.741 55.000 14.40 1.93 41.48 5.34
964 1021 0.456221 CGTCGGTTGATCTAGCACCT 59.544 55.000 7.13 0.00 0.00 4.00
965 1022 0.454600 TCGTCGGTTGATCTAGCACC 59.545 55.000 7.13 1.31 0.00 5.01
966 1023 1.546834 GTCGTCGGTTGATCTAGCAC 58.453 55.000 7.13 3.74 0.00 4.40
967 1024 0.098200 CGTCGTCGGTTGATCTAGCA 59.902 55.000 7.13 0.00 0.00 3.49
968 1025 2.856089 CGTCGTCGGTTGATCTAGC 58.144 57.895 0.00 0.00 0.00 3.42
980 1037 3.885521 CTAGCCGTCCCCGTCGTC 61.886 72.222 0.00 0.00 0.00 4.20
1035 1094 4.465446 CCGAGGAGGAGGAGGCCA 62.465 72.222 5.01 0.00 45.00 5.36
1158 1223 2.248431 GCCGACTTGTTCACGCAC 59.752 61.111 0.00 0.00 0.00 5.34
1263 1328 1.153997 GAGGAAGTCCACGACGAGC 60.154 63.158 0.00 0.00 37.67 5.03
1272 1337 2.507324 GACTGCGCGAGGAAGTCC 60.507 66.667 12.10 0.00 0.00 3.85
1290 1355 2.258748 GAAGGAAAGGGAGGCCGAGG 62.259 65.000 0.00 0.00 0.00 4.63
1305 1370 3.330720 AGCTTGGACGGGGGAAGG 61.331 66.667 0.00 0.00 0.00 3.46
1389 1454 0.462759 GGCCGATGGACTTGAGGAAG 60.463 60.000 0.00 0.00 35.07 3.46
1452 1517 2.915659 AGGTCGCGGAACCACTGA 60.916 61.111 18.13 0.00 42.12 3.41
1665 1730 3.621805 ACCACGATGTCCACCGCA 61.622 61.111 0.00 0.00 0.00 5.69
1992 2057 4.096003 CCCTTCATCCCGCACCGT 62.096 66.667 0.00 0.00 0.00 4.83
2105 2170 2.001269 GGGTGGCAGTATGGTCCCT 61.001 63.158 0.07 0.00 35.86 4.20
2169 2234 1.885887 ACATCACGTTTTCCCCACATG 59.114 47.619 0.00 0.00 0.00 3.21
2173 2238 3.822940 ACTAAACATCACGTTTTCCCCA 58.177 40.909 0.00 0.00 45.79 4.96
2266 2333 5.105473 GCTACACCTACACATAAGAGTCCAA 60.105 44.000 0.00 0.00 0.00 3.53
2269 2336 4.497674 CGGCTACACCTACACATAAGAGTC 60.498 50.000 0.00 0.00 35.61 3.36
2330 2397 8.556213 AAATTTTCAGCAAAAGCATATGATGT 57.444 26.923 6.97 0.00 34.92 3.06
2352 2419 7.690256 AGGTTCTAGGTTGTAGTCAATGAAAT 58.310 34.615 0.00 0.00 35.92 2.17
2359 2426 6.488769 TGAAAAGGTTCTAGGTTGTAGTCA 57.511 37.500 0.00 0.00 34.60 3.41
2481 2549 5.944013 TCTGCATAGTTGTATAGCGAGATC 58.056 41.667 0.00 0.00 0.00 2.75
2501 2569 1.066573 AGGTCGCTGTTGGAGATTCTG 60.067 52.381 0.00 0.00 0.00 3.02
2514 2582 1.079503 GAGAAAATTCGCAGGTCGCT 58.920 50.000 0.00 0.00 39.08 4.93
2554 2622 1.658686 GGTGACGACCTCTCGCATCT 61.659 60.000 0.00 0.00 44.33 2.90
2569 2637 4.373116 GCGAGGAGCGTTGGGTGA 62.373 66.667 0.00 0.00 43.41 4.02
2601 2669 2.901249 TCGTCCCTTTGATTCGGATTC 58.099 47.619 0.00 0.00 0.00 2.52
2718 2792 2.958355 TCGTCCGGTATAAGGTTTAGGG 59.042 50.000 0.00 0.00 0.00 3.53
2727 2801 1.132262 GTTCGTGGTCGTCCGGTATAA 59.868 52.381 0.00 0.00 38.33 0.98
2757 2847 2.437002 GGATGGCAACGGCGGTAA 60.437 61.111 13.24 0.00 42.47 2.85
2767 2857 3.620300 GACGACGACACGGATGGCA 62.620 63.158 0.00 0.00 37.61 4.92
2774 2864 3.642008 GAGGGACGACGACGACACG 62.642 68.421 15.32 7.07 41.74 4.49
2901 3007 2.860690 TACATCGACAGTGTCCGCGC 62.861 60.000 17.57 0.00 0.00 6.86
2979 3085 2.802667 CGCCAAGATCGACAAGCGG 61.803 63.158 8.69 0.00 39.89 5.52


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.